Aerobic granular sludge (AGS) is an advanced biofilm-based technology for wastewater treatment. Diffusion of substrates into the granules is a key aspect of this technology. Domestic wastewater contains soluble organic substrates of different sizes that could potentially diffuse into the granules. In this study, the relation between the molecular weight of a substrate and its diffusion coefficient within the granule was studied with model substrates (polyethylene glycols (PEGs) with a molecular weight between 62 and 10 000 Da). The diffusion coefficients of the model substrates within granules from a full-scale installation were measured with the ‘transient uptake of a non-reactive solute’ method. The diffusion coefficients in the granules were not significantly different from the diffusion coefficients in water, at least up to 4000 Da molecular weight. This indicates that these PEGs were not obstructed by the granule matrix. The 10 kDa PEG behaved differently from the lighter PEGs, as it could not penetrate the entire granule. Furthermore, the granule structure was characterized with Environmental Scanning Electron Microscopy (ESEM). The granules displayed an open structure with large macropores and semi-solid regions, which contained microbial cells. The diffusion results suggest that most diffusing molecules were unobstructed in the macropores and barely obstructed in the semi-solid regions. Only the diffusion of the 10 kDa PEG seemed to be hindered by the semi-solid regions, but not by the macropores. Lastly, the apparent molecular weight distribution of domestic wastewater soluble COD was determined with ultrafiltration membranes of 100, 10, and 1 kDa molecular weight cut-off. The influent fractionation revealed that a large part (61–69%) of the influent soluble COD was lighter than 1 kDa. As molecules lighter than 1 kDa diffuse easily, the majority of the influent soluble COD can be considered as diffusible COD. These findings provide new insight into the availability of influent COD for granular sludge.